http://lod.bco-dmo.org/id/dataset/745518
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2018-09-04
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Microbial eukaryotic focused metatranscriptome data from seawater collected in coastal California in May of 2015
2018-10-15
publication
2018-10-15
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-05-11
publication
https://doi.org/10.26008/1912/bco-dmo.745518.2
David Caron
University of Southern California
principalInvestigator
Sarah K. Hu
University of Southern California
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Caron, D., Hu, S. (2020) Microbial eukaryotic focused metatranscriptome data from seawater collected in coastal California in May of 2015. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2) Version Date 2018-10-15 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.745518.2 [access date]
Dataset Description: Seawater was collected via Niskin bottles mounted with a CTD from the San Pedro Ocean Time-series (SPOT) station off the coast of Southern California near the surface (5 m), 150 and 890 m, in late May 2015. Raw sequence data was generated as part of a metatranscriptome study targeting the protistan community. Raw sequences are available at the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) database (SRA Study ID: SRP110974, BioProject: PRJNA391503).
These data were published in Hu et al. (2018). Methods and Sampling: <p>Seawater was collected from the San Pedro Ocean Time-series (SPOT) station off the coast of Southern California near the surface (5 m), 150 and 890 m, in late May 2015. Briefly, seawater was pre-filtered (80 mm) into 20 L carboys to minimize the presence of multicellular eukaryotes. Replicate samples (ranging in volume from 1.5-3.5 L) from each depth were filtered onto sterile GF/F filters (nominal pore size 0.7 mm, Whatman, International Ltd. Florham Park, NJ). While we cannot avoid some impact that sample handling (i.e., bringing samples to the surface) may have had on our results, filters were immediately placed in 1.5 mL of lysis buffer and flash frozen in liquid nitrogen in &lt; 40 min and away from light to minimize RNA degradation.</p>
<p>Total RNA was extracted from each filter using a DNA/RNA AllPrep kit (Qiagen, Valencia, CA, #80204) with an in-line genomic DNA removal step (RNase-free DNase reagents, Qiagen #79254) (dx.doi.org/10.17504/protocols.io.hk3b4yn). Extracted RNA was quality checked and low biomass samples were pooled. Six replicates were processed and sequenced from the surface, while pairs of filters were pooled for either 150 or 890 m, yielding 3 and 4 replicates respectively (Supporting Information Table S1). RNA concentrations were normalized before library preparation (Supporting Information). ERCC spike-in was added before sequence library preparation with Kapa’s Stranded mRNA library preparation kit using poly-A tail selection beads to select for eukaryotic mRNA (Kapa Biosystems, Inc., Wilmington, MA, #KK8420).</p>
<p>Also see:</p>
<p>https://www.protocols.io/view/sample-collection-from-the-field-for-downstream-mo-hisb4eehttps://www.protocols.io/view/rna-and-optional-dna-extraction-from-environmental-hk3b4yn<br />
<br />
The associated assembly files can be found at Zenodo (see Hu, S. K. (2017), DOI:&nbsp;10.5281/zenodo.1202041).&nbsp; The assembly files were also published in the journal publication Hu, et al. (2018).<br />
<br />
Related code can be found in the github repository https://github.com/shu251/SPOT_metatranscriptome.&nbsp; The version of the code used for these publications can be found in the Supplemental Files section of this page.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1737409 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1737409
completed
David Caron
University of Southern California
213-740-0203
Dornsife College of Letters, Arts, and Sciences 3616 Trousdale Parkway
Los Angeles
CA
90089
USA
dcaron@usc.edu
pointOfContact
Sarah K. Hu
University of Southern California
skhu@tamu.edu
pointOfContact
asNeeded
Dataset Version: 2
Unknown
SRA_run
SRA_run_link
SRA_study
bioproject_accession
biosample_accession
library_ID
title
sample_name
library_strategy
library_source
library_selection
library_layout
platform
instrument_model
design_description
filetype
filename
filename2
HiSeq
theme
None, User defined
accession number
external_link
sample description
file_name
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Niskin bottle
instrument
BCO-DMO Standard Instruments
SPOT_Yellowfin_Cruises
service
Deployment Activity
San Pedro Ocean Time Series
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Protistan, prokaryotic, and viral processes at the San Pedro Ocean Time-series
https://osprey.bco-dmo.org/project/743049
Protistan, prokaryotic, and viral processes at the San Pedro Ocean Time-series
<p>Planktonic marine microbial communities consist of a diverse collection of bacteria, archaea, viruses, protists (phytoplankton and protozoa) and small animals (metazoan). Collectively, these species are responsible for virtually all marine pelagic primary production where they form the basis of food webs and carry out a large fraction of respiratory processes. Microbial interactions include the traditional role of predation, but recent research recognizes the importance of parasitism, symbiosis and viral infection. Characterizing the response of pelagic microbial communities and processes to environmental influences is fundamental to understanding and modeling carbon flow and energy utilization in the ocean, but very few studies have attempted to study all of these assemblages in the same study. This project is comprised of long-term (monthly) and short-term (daily) sampling at the San Pedro Ocean Time-series (SPOT) site. Analysis of the resulting datasets investigates co-occurrence patterns of microbial taxa (e.g. protist-virus and protist-prokaryote interactions, both positive and negative) indicating which species consistently co-occur and potentially interact, followed by examination gene expression to help define the underlying mechanisms. This study augments 20 years of baseline studies of microbial abundance, diversity, rates at the site, and will enable detection of low-frequency changes in composition and potential ecological interactions among microbes, and their responses to changing environmental forcing factors. These responses have important consequences for higher trophic levels and ocean-atmosphere feedbacks. The broader impacts of this project include training graduate and undergraduate students, providing local high school student with summer lab experiences, and PI presentations at local K-12 schools, museums, aquaria and informal learning centers in the region. Additionally, the PIs advise at the local, county and state level regarding coastal marine water quality.</p>
<p>This research project is unique in that it is a holistic study (including all microbes from viruses to small metazoa) of microbial species diversity and ecological activities, carried out at the SPOT site off the coast of southern California. In studying all microbes simultaneously, this work aims to identify important ecological interactions among microbial species, and identify the basis(es) for those interactions. This research involves (1) extensive analyses of prokaryote (archaean and bacterial) and eukaryote (protistan and micro-metazoan) diversity via the sequencing of marker genes, (2) studies of whole-community gene expression by eukaryotes and prokaryotes in order to identify key functional characteristics of microorganismal groups and the detection of active viral infections, and (3) metagenomic analysis of viruses and bacteria to aid interpretation of transcriptomic analyses using genome-encoded information. The project includes exploratory metatranscriptomic analysis of poorly-understood aphotic and hypoxic-zone protists, to examine their stratification, functions and hypothesized prokaryotic symbioses.</p>
SPOT
largerWorkCitation
project
eng; USA
oceans
San Pedro Ocean Time Series
-118.4
-118.4
33.55
33.55
2015-05-20
2015-05-20
San Pedro Channel off the coast of Los Angeles
0
BCO-DMO catalogue of parameters from Microbial eukaryotic focused metatranscriptome data from seawater collected in coastal California in May of 2015
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/805470.rdf
Name: SRA_run
Units: unitless
Description: <p>SRA Run identifier at NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/805471.rdf
Name: SRA_run_link
Units: unitless
Description: <p>URL for SRA Run Page at NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/805472.rdf
Name: SRA_study
Units: unitless
Description: <p>SRA study identifier at NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/805473.rdf
Name: bioproject_accession
Units: unitless
Description: <p>BioProject accesion number at NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/805474.rdf
Name: biosample_accession
Units: unitless
Description: <p>BioSample accession number at NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/805475.rdf
Name: library_ID
Units: unitless
Description: <p>SRA title</p>
http://lod.bco-dmo.org/id/dataset-parameter/805476.rdf
Name: title
Units: unitless
Description: <p>Descriptive title of SRA accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/805477.rdf
Name: sample_name
Units: unitless
Description: <p>Sample name</p>
http://lod.bco-dmo.org/id/dataset-parameter/805478.rdf
Name: library_strategy
Units: unitless
Description: <p>Library strategy ("AMPLICON")</p>
http://lod.bco-dmo.org/id/dataset-parameter/805479.rdf
Name: library_source
Units: unitless
Description: <p>Library source ("TRANSCRIPTOMIC" or "GENOMIC")</p>
http://lod.bco-dmo.org/id/dataset-parameter/805480.rdf
Name: library_selection
Units: unitless
Description: <p>Library selection ("PCR")</p>
http://lod.bco-dmo.org/id/dataset-parameter/805481.rdf
Name: library_layout
Units: unitless
Description: <p>Library layout ("paired")</p>
http://lod.bco-dmo.org/id/dataset-parameter/805482.rdf
Name: platform
Units: unitless
Description: <p>Sequencing platform ("Illumina")</p>
http://lod.bco-dmo.org/id/dataset-parameter/805483.rdf
Name: instrument_model
Units: unitless
Description: <p>Sequencing instrument model ("Illumina MiSeq")</p>
http://lod.bco-dmo.org/id/dataset-parameter/805484.rdf
Name: design_description
Units: unitless
Description: <p>Sequencing design description</p>
http://lod.bco-dmo.org/id/dataset-parameter/805485.rdf
Name: filetype
Units: unitless
Description: <p>Type of files</p>
http://lod.bco-dmo.org/id/dataset-parameter/805486.rdf
Name: filename
Units: unitless
Description: <p>Name of file 1 (see NCBI for access)</p>
http://lod.bco-dmo.org/id/dataset-parameter/805487.rdf
Name: filename2
Units: unitless
Description: <p>Name of file 2 (see NCBI for access)</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
12079
https://darchive.mblwhoilibrary.org/bitstream/1912/25760/1/dataset-745518_microbial-eukaryotic-focused-metatranscriptome-data__v2.tsv
download
https://doi.org/10.26008/1912/bco-dmo.745518.2
download
onLine
dataset
<p>Seawater was collected from the San Pedro Ocean Time-series (SPOT) station off the coast of Southern California near the surface (5 m), 150 and 890 m, in late May 2015. Briefly, seawater was pre-filtered (80 mm) into 20 L carboys to minimize the presence of multicellular eukaryotes. Replicate samples (ranging in volume from 1.5-3.5 L) from each depth were filtered onto sterile GF/F filters (nominal pore size 0.7 mm, Whatman, International Ltd. Florham Park, NJ). While we cannot avoid some impact that sample handling (i.e., bringing samples to the surface) may have had on our results, filters were immediately placed in 1.5 mL of lysis buffer and flash frozen in liquid nitrogen in &lt; 40 min and away from light to minimize RNA degradation.</p>
<p>Total RNA was extracted from each filter using a DNA/RNA AllPrep kit (Qiagen, Valencia, CA, #80204) with an in-line genomic DNA removal step (RNase-free DNase reagents, Qiagen #79254) (dx.doi.org/10.17504/protocols.io.hk3b4yn). Extracted RNA was quality checked and low biomass samples were pooled. Six replicates were processed and sequenced from the surface, while pairs of filters were pooled for either 150 or 890 m, yielding 3 and 4 replicates respectively (Supporting Information Table S1). RNA concentrations were normalized before library preparation (Supporting Information). ERCC spike-in was added before sequence library preparation with Kapa’s Stranded mRNA library preparation kit using poly-A tail selection beads to select for eukaryotic mRNA (Kapa Biosystems, Inc., Wilmington, MA, #KK8420).</p>
<p>Also see:</p>
<p>https://www.protocols.io/view/sample-collection-from-the-field-for-downstream-mo-hisb4eehttps://www.protocols.io/view/rna-and-optional-dna-extraction-from-environmental-hk3b4yn<br />
<br />
The associated assembly files can be found at Zenodo (see Hu, S. K. (2017), DOI:&nbsp;10.5281/zenodo.1202041).&nbsp; The assembly files were also published in the journal publication Hu, et al. (2018).<br />
<br />
Related code can be found in the github repository https://github.com/shu251/SPOT_metatranscriptome.&nbsp; The version of the code used for these publications can be found in the Supplemental Files section of this page.</p>
Specified by the Principal Investigator(s)
<p>Sequence adapters, low quality (phred score &lt; 10, from 5’ and 3’ ends, and within a 25 bp sliding window) or short sequences (&lt; 50 bps), and sequences containing more than 50 consecutive As or Ts were removed using Trimmomatic v. 0.32 (Bolger et al., 2014). All quality trimmed sequences were aligned to ERCC sequences using ‘align_and_estimate_abun- dance.pl’ in the Trinity v. 2.1.1 (Grabherr et al., 2011) package. Reads that were aligned to ERCC sequences were removed using a custom PERL script (available: https://github.com/shu251/SPOT_metatranscriptome).</p>
Specified by the Principal Investigator(s)
[Changes discussed with and reviewed by the data submitter]
* added a conventional header with dataset name, PI name, version date
* modified parameter names to conform with BCO-DMO naming conventions
* blank values in this dataset are displayed as "nd" for "no data." nd is the default missing data identifier in the BCO-DMO system.
* removed columns "object_status" and blank columns "filename3" and "filename4."
* Added column SRA_ID_link to the SRA run at NCBI
* removed column "assembly" which had values of "See related publication for access to assembly files" This information was included in the Methods & Sampling section of the methodology and further explained.
* For curatorial purposes BCO-DMO forked the github code repository https://github.com/shu251/SPOT_metatranscriptome and created a github release (see https://github.com/BCODMO/SPOT_metatranscriptome/releases/tag/bcodmo_v1). The release .zip file was downloaded to BCO-DMO's servers and added to the dataset landing page as a supplemental file to satisfy NSF OCE sharing requirements.
* changes in version 2: data for bioproject PRJNA608423 added to the dataset.
Specified by BCO-DMO Data Managers
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
HiSeq
HiSeq
PI Supplied Instrument Name: HiSeq PI Supplied Instrument Description:HiSeq High Output 125 bp PE sequencing was performed at UPC Genome Core at University of Southern California, Los Angeles, CA (BioProject: PRJNA391503). Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
PI Supplied Instrument Name: Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
Cruise: SPOT_Yellowfin_Cruises
SPOT_Yellowfin_Cruises
R/V Yellowfin
R/V Yellowfin
vessel
R/V Yellowfin
R/V Yellowfin
vessel